(1/n) Excited to share close collab w @bloodgenes.bsky.social led by Varshini & Chun-jie et al How to induce expression of key genes while silencing much of the genome during Erythropoiesis? A: Matchmaker CREs load cohesin near key genes to promote looping & exp: www.biorxiv.org/content/10.6...

A really cool preprint from Joanna Wysocka's lab showing that housekeeping genes use distal enhancers as dosage buffers against TF fluctuations, but only during critical cell fate transitions. Makes so much sense! www.biorxiv.org/content/10.6...

Enhancer buffering protects dosage-sensitive housekeeping genes during vulnerable developmental transitions

Housekeeping genes maintain robust expression across cell types despite dynamic transcription factor fluctuations, yet their haploinsufficiency is associated with many tissue-specific developmental di...

biorxiv.org

New preprint from Shendure Lab on Locus-Scale aka Long-@$$ MPRAs led by the amazing Abby McGee & @carinabiar.bsky.social Most MPRAs test ~300 bp fragments next to a promoter. But real enhancers are bigger, act combinatorially and from a distance. 1/n www.biorxiv.org/content/10.6...

Thrilled to post thread re: new single-cell lineage of mouse embryo reconstructed w/ DNA Typewriter. One animal, zygote to late organogenesis (E13.5). Tree has 1,340,794 transcriptionally profiled, annotated tips (cells), 1,142,588 dated internal nodes, rooted at zygote 1/n

Avocados come in 2 varieties - A-types start each day female and switch to male midday. B-types do the reverse. In work just published from the last chapter of my PhD, we show this system evolved 40+million yrs ago and is regulated by alleles of 1 transcription factor www.pnas.org/doi/10.1073/...

Balanced polymorphism in a floral transcription factor underlies the ancient rhythm of daily sex alternation in avocado | PNAS

In avocado and certain wild relatives in Lauraceae, a highly synchronized daily rhythm of floral sex timing promotes cross-pollination between two ...

pnas.org

🚨 Job Alert - Please share 🙏 Interested in 3D gene regulation in development & evolution? 🤓🧬 💥 Our lab at @cabd-upo-csic.bsky.social is expanding! ✅ 4 years fully funded PhD position 💻🧪 Experimental or computational backgrounds welcome 👇 Details below #PhDPosition #PhDOpportunity #AcademicJobs

Now online! Robust regulatory interplay of enhancers, facilitators, and promoters in a native chromatin context

Robust regulatory interplay of enhancers, facilitators, and promoters in a native chromatin context

Using an in situ genome-rewriting platform, Zhou et al. demonstrate that precise transcriptional regulation of the NMU promoter is governed by a 3D regulatory hub comprising a core retroviral LTR enhancer, a decoy LTR promoter, and activity-boosting “facilitator” elements.

dlvr.it

@mileshuseyin.bsky.social and the lab have put together a comprehensive protocol for genome-wide Micro-C and for Region-Capture Micro-C in @natprot.nature.com : www.nature.com/articles/s41... See also the GitHub for a user-friendly end-to-end computational pipeline: github.com/ahansenlab/M...

Nature Protocols@natprot.nature.com · last mo.

New Article! Mapping 3D genome organization at nucleosome-scale with Micro-C and Region Capture Micro-C (RCMC)

We have an open professor position at my institute, the Institute for Quantitative Biosciences, The University of Tokyo! www.iqb.u-tokyo.ac.jp/recruiting/2...

Frank Grosveld has been a giant in the field of long-range gene regulation. Inspirational to me and I am sure for many others. Rest in peace.

Lluis Montoliu@lluismontoliu.bsky.social · 2mo ago

Frank Grosveld, born in 1948, passed away last Friday. He was a colossal scientist in the transcriptional control of gene expression during development and helped us understand the complex regulation of beta-globin genes. His work will remain as a reference. May he rest in peace.

Our latest is out in Nature Genetics with @soumyakundu.bsky.social @anshulkundaje.bsky.social and @sbmontgom.bsky.social ! We built a resource of predicted variant effects on chromatin accessibility, and FLARE to identify disease variants with extreme effects. www.nature.com/articles/s41...

Decoding common and rare noncoding variant effects across cellular and developmental contexts - Nature Genetics

This study contributes a resource of predicted effects of noncoding variants on chromatin accessibility and a method to identify noncoding variants with extreme regulatory effects, with application to...

nature.com

(1/n) Very excited to share tri-lab collab (Mirny & Zechner) led by Harvey, Henrik & Jack: Q: How do enhancers & promoters interact in space (contact vs. action-at-a-distance) and time (stable vs. transient)? A: Transient E-P contact (~25-42 nm lasting ~10-20 sec): www.biorxiv.org/content/10.6...

Austria is a clear outlier - not surprisingly. the-one-percent.qedscience.com

I first met Neil Shubin 30 years ago when he was digging for fossils of our fishy ancestors in Pennsylvania road cuts. Now he's becoming president of the National Academy of Sciences. We talked about taking the helm of the 163-year-old organization at this fraught moment. Gift link: nyti.ms/4giD3FX

Congratulations to our graduate student, Sarah Espinoza, for receiving the NICHD Ruth L. Kirschstein NRSA F31 Award for predoctoral trainees! www.kvonlab.org/members

Updated GRC Developmental Biology 2027 flyer/poster with the latest roster of invited speakers. 🌱🐟🧬🐭🪰🧪🧫 Come join us to discuss the latest in #devbio at the Renaissance Tuscany Il Ciocco Resort, Jan 17-22 ! #GRCDevBio2027

Christian Mosimann@chrmosimann.bsky.social · 3mo ago

*** GRC Developmental Biology 2027 - Jan 17-22 @ Renaissance Tuscany Il Ciocco Resort *** Join us for a fabulous 2027 Gordon Conference on all things #devbio & the trainee-led GRS! More info on registration, abstract submission, et al., here: www.grc.org/developmenta... #GRCDevBio2027 🧬🐭🐟🪰🌱❤️

Looks like the 2027 Dev Bio GRC is shaping up to be another good one: www.grc.org/developmenta...

Is distal gene activation by enhancers inherently different from promoter-proximal activation? We propose not. But both cohesin and cooperativity are important aspects of how transcription is affected. Happy to share our recent preprint (thread below) 1/ www.biorxiv.org/content/10.6...

📣 Preprint alert! We developed a method to analyze concurrent interactions between multiple chromatin regions at single alleles at sub-nucleosome resolution (multi-way Micro-Capture-C, mwMCC) & used this to study structural synergy within super-enhancers. 1/14 www.biorxiv.org/content/10.6...

Why can't we explain enhancer action despite 2 decades of chromosome conformation technologies? 😬 Our new study spearheaded by Leonid Mirny's group points to a flaw in our assumptions, and to a solution from physical principles By @timothyfoldes.bsky.social 💻& @karissalhansen.bsky.social 🧪 🧵👇

If it walks like a duck and develops like a duck ... the enhancers might still align to humans 🥚🦆 (chicken, actually, but you get the picture) Fun collaboration led by Stella Kyomen and @marketa-kau.bsky.social at @mpi-evolbio.bsky.social

MPI for Evolutionary Biology@mpi-evolbio.bsky.social · 3mo ago

Facial diversity in birds and mammals doesn’t just come from different signals – but from how cells respond to them. A new study in Science Advances shows evolution acts on both: signal placement and cellular interpretation. More Info: www.evolbio.mpg.de/3879733/news... @marketa-kau.bsky.social

Although cohesin-sensitive, long-range enhancer activation is equivalent in nature to proximal activation. Cooperativity can arise from different levels of activation inputs operating on a non-linear response function. @eliasfriman.bsky.social @uoe-igc.bsky.social www.biorxiv.org/content/10.6...

🔔This Wednesday we are excited to have three amazing ECR talks at #FragileNucleosome by Ujani, @ewholling.bsky.social & @germainekaram.bsky.social ! Don't forget to subscribe to our series! us06web.zoom.us/webinar/regi...

They wrote an NIH application proposing to sequence the H. influenzae genome by shotgun sequencing. The study section scored it relatively poorly because the reviewers thought this approach would not work. Fortunately, the sequence was complete by the time the application was reviewed. 3/4

Huge congratulations to our postdoc Zhuoxin Chen on receiving the K99/R00 Pathway to Independence Award after a long wait! She is amazing and is currently on a job market. www.bio.uci.edu/uci-postdoct...

UCI Postdoctoral Fellow Zhuoxin Chen Awarded NIH K99/R00 Pathway to Independence Award - Charlie Dunlop School of Biological Sciences

Zhuoxin Chen, a postdoctoral fellow in the lab of Assistant Professor Evgeny Kvon at the Department of Developmental & Cell Biology at the Charlie Dunlop School of Biological Sciences, has been awarde...

bio.uci.edu

Huge congratulations to Grace Bower @gracebower.bsky.social who successfully defended her PhD thesis today. You rock!

📖 The final version of our paper is out in press Cohesin cofactor dosage sets the rate of loop extrusion, rendering genome folding tunable yet vulnerable to genetic disruption authors.elsevier.com/a/1m%7EU03vV... or www.cell.com/molecular-ce...

Cohesin cofactor dosage sets the rate of loop extrusion, rendering genome folding tunable yet vulnerable to genetic disruption

Shah, Tortora, et al. show that cells can dial the rate of cohesin loop extrusion by balancing the relative dosage of NIPBL and PDS5. Their models provide a quantitative mechanistic basis for the gene...

cell.com

Elphege Nora Lab at UCSF@elphegenoralab.bsky.social · 12mo ago

New preprint with @gfudenberg.bsky.social We find the rate of cohesin loop extrusion in cells is set by NIPBL dosage and tunes many aspects of chromosome folding. This provides a molecular basis for NIPBL haploinsufficiency in humans. 🧵👇 www.biorxiv.org/content/10.1...

New paper in Genes & Dev: we dissected how Sox2 — a key pluripotency TF — is regulated by a distal enhancer cluster (SCR) 100 kb away. The results challenge simple models of cohesin-mediated loop extrusion of gene regulation. genesdev.cshlp.org/content/earl... 🧵

De novo formation of cis-regulatory contacts in the absence of NIPBL-driven chromatin loop extrusion www.nature.com/articles/s41...

De novo formation of cis-regulatory contacts in the absence of NIPBL-driven chromatin loop extrusion - Nature Genetics

The authors deplete the cohesin activator NIPBL during the mitosis-to-G1-phase transition. They observe that structural loop formation is impaired proportionally to loop length, while gene activation ...

nature.com

Our bat–mouse limb paper is now on bioRxiv!
🦇https://www.biorxiv.org/content/10.64898/2026.04.07.717074v2 This was a collaborative effort across the @nadavahituv.bsky.social Nicola Illing, Dorit Hockman, Guy Kelman, Tommy Kaplan labs and my lab at @washugenetics.bsky.social